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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
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Hi, thank you for developing this excellent software. I encountered an issue while running isoquant.py to analyze Oxford Nanopore data. Could you please let me know how to resolve it? I would greatly…
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I'm trying to run some nanopore test reads through mothur but am getting stuck at the very beginning. I was going to follow your pacbio example so was trying to start with fastq.info. My data are conc…
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Hello everyone!
My Name is Azlan and i am currently analyzing our ONT Data. I wanted to use uxm and wgbs_tools to further investigate the methylation status in different samples and just wanted to…
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Not much Nanopore data has been run using the pipeline, so it's hard to say how appropriate the default parameters are for these data vs Illumina. However, some suggestions based on the [`setDadaOpt`]…
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Hi,
I was wondering if there might be a recommendation on using herro corrected reads with assembly mode 2, as opposed to just blindly using config `Nanopore-Phased-R10-Fast-Nov2022` and `--Kmers.k …
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Is there anything in the structure of amptk that would prohibit using Nanopore amplicon data as input?
Fragment lengths are ~1500 bp. Input fastq are already adapter and quality trimmed and demulti…
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Review existing tools in the pipeline if they can take in Nanopore data. If not, find a suitable alternative for long reads.
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My name is Jemima and I recently started a PhD working on stool and vaginal samples from a clinical trial in SSA. I am currently working on sequencing the full 16s gene on nanopore platform. I have s…
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Hi, not an issue but will this tool work with bacterial transcriptome? I read through the manual and couldn't find an answer. Since bacterial species don't have introns will this program have any nega…